Back to Multiple platform build/check report for BioC 3.21: simplified long |
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This page was generated on 2025-10-13 11:38 -0400 (Mon, 13 Oct 2025).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) | x86_64 | 4.5.1 (2025-06-13) -- "Great Square Root" | 4833 |
merida1 | macOS 12.7.5 Monterey | x86_64 | 4.5.1 RC (2025-06-05 r88288) -- "Great Square Root" | 4614 |
kjohnson1 | macOS 13.6.6 Ventura | arm64 | 4.5.1 Patched (2025-06-14 r88325) -- "Great Square Root" | 4555 |
kunpeng2 | Linux (openEuler 24.03 LTS) | aarch64 | R Under development (unstable) (2025-02-19 r87757) -- "Unsuffered Consequences" | 4586 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 799/2341 | Hostname | OS / Arch | INSTALL | BUILD | CHECK | BUILD BIN | ||||||||
GeDi 1.4.0 (landing page) Annekathrin Nedwed
| nebbiolo1 | Linux (Ubuntu 24.04.3 LTS) / x86_64 | OK | OK | ERROR | |||||||||
merida1 | macOS 12.7.5 Monterey / x86_64 | OK | OK | ERROR | OK | |||||||||
kjohnson1 | macOS 13.6.6 Ventura / arm64 | OK | OK | ERROR | OK | |||||||||
kunpeng2 | Linux (openEuler 24.03 LTS) / aarch64 | OK | OK | ERROR | ||||||||||
To the developers/maintainers of the GeDi package: - Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/GeDi.git to reflect on this report. See Troubleshooting Build Report for more information. - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: GeDi |
Version: 1.4.0 |
Command: /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GeDi_1.4.0.tar.gz |
StartedAt: 2025-10-12 23:30:28 -0400 (Sun, 12 Oct 2025) |
EndedAt: 2025-10-12 23:39:22 -0400 (Sun, 12 Oct 2025) |
EllapsedTime: 534.8 seconds |
RetCode: 1 |
Status: ERROR |
CheckDir: GeDi.Rcheck |
Warnings: NA |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD check --install=check:GeDi.install-out.txt --library=/home/biocbuild/bbs-3.21-bioc/R/site-library --timings GeDi_1.4.0.tar.gz ### ############################################################################## ############################################################################## * using log directory ‘/home/biocbuild/bbs-3.21-bioc/meat/GeDi.Rcheck’ * using R version 4.5.1 (2025-06-13) * using platform: x86_64-pc-linux-gnu * R was compiled by gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0 * running under: Ubuntu 24.04.3 LTS * using session charset: UTF-8 * checking for file ‘GeDi/DESCRIPTION’ ... OK * this is package ‘GeDi’ version ‘1.4.0’ * package encoding: UTF-8 * checking package namespace information ... OK * checking package dependencies ... INFO Imports includes 29 non-default packages. Importing from so many packages makes the package vulnerable to any of them becoming unavailable. Move as many as possible to Suggests and use conditionally. * checking if this is a source package ... OK * checking if there is a namespace ... OK * checking for hidden files and directories ... OK * checking for portable file names ... OK * checking for sufficient/correct file permissions ... OK * checking whether package ‘GeDi’ can be installed ... OK * checking installed package size ... OK * checking package directory ... OK * checking ‘build’ directory ... OK * checking DESCRIPTION meta-information ... OK * checking top-level files ... OK * checking for left-over files ... OK * checking index information ... OK * checking package subdirectories ... OK * checking code files for non-ASCII characters ... OK * checking R files for syntax errors ... OK * checking whether the package can be loaded ... OK * checking whether the package can be loaded with stated dependencies ... OK * checking whether the package can be unloaded cleanly ... OK * checking whether the namespace can be loaded with stated dependencies ... OK * checking whether the namespace can be unloaded cleanly ... OK * checking loading without being on the library search path ... OK * checking whether startup messages can be suppressed ... OK * checking dependencies in R code ... OK * checking S3 generic/method consistency ... OK * checking replacement functions ... OK * checking foreign function calls ... OK * checking R code for possible problems ... OK * checking Rd files ... OK * checking Rd metadata ... OK * checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors: buildClusterGraph.Rd: igraph dot-graphMetricsGenesetsDT.Rd: igraph getAnnotation.Rd: STRINGdb getId.Rd: STRINGdb getPPI.Rd: STRINGdb getStringDB.Rd: STRINGdb Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages. * checking for missing documentation entries ... OK * checking for code/documentation mismatches ... OK * checking Rd \usage sections ... OK * checking Rd contents ... OK * checking for unstated dependencies in examples ... OK * checking contents of ‘data’ directory ... OK * checking data for non-ASCII characters ... OK * checking data for ASCII and uncompressed saves ... OK * checking files in ‘vignettes’ ... OK * checking examples ... ERROR Running examples in ‘GeDi-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: getAnnotation > ### Title: Get the annotation of a STRINGdb object > ### Aliases: getAnnotation > > ### ** Examples > > stringdb <- getStringDB(9606) > stringdb *********** STRING - https://string-db.org *********** (Search Tool for the Retrieval of Interacting Genes/Proteins) version: 12.0 species: 9606 ............please wait............ trying URL 'https://stringdb-downloads.org/download/protein.info.v12.0/9606.protein.info.v12.0.txt.gz' Warning in download.file(urlStr, temp) : URL 'https://stringdb-downloads.org/download/protein.info.v12.0/9606.protein.info.v12.0.txt.gz': status was 'SSL peer certificate or SSH remote key was not OK' Error in download.file(urlStr, temp) : cannot open URL 'https://stringdb-downloads.org/download/protein.info.v12.0/9606.protein.info.v12.0.txt.gz' Calls: <Anonymous> ... get_proteins -> downloadAbsentFile -> download.file Execution halted * checking for unstated dependencies in ‘tests’ ... OK * checking tests ... Running ‘testthat.R’ ERROR Running the tests in ‘tests/testthat.R’ failed. Last 13 lines of output: Error in `download.file(urlStr, temp)`: cannot open URL 'https://stringdb-downloads.org/download/protein.aliases.v12.0/9606.protein.aliases.v12.0.txt.gz' Backtrace: ▆ 1. └─GeDi::getAnnotation(stringdb) at test-downloadPPI.R:24:3 2. └─stringdb$get_aliases() 3. └─STRINGdb::downloadAbsentFile(...) 4. └─utils::download.file(urlStr, temp) ── Failure ('test-gs_histogram.R:27:3'): gsHistogram runs correctly ──────────── `histogram` has type 'object', not 'list'. ── Failure ('test-gs_histogram.R:30:3'): gsHistogram runs correctly ──────────── `histogram` has type 'object', not 'list'. [ FAIL 8 | WARN 13 | SKIP 0 | PASS 176 ] Error: Test failures Execution halted * checking for unstated dependencies in vignettes ... OK * checking package vignettes ... OK * checking re-building of vignette outputs ... OK * checking PDF version of manual ... OK * DONE Status: 2 ERRORs, 1 NOTE See ‘/home/biocbuild/bbs-3.21-bioc/meat/GeDi.Rcheck/00check.log’ for details.
GeDi.Rcheck/00install.out
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.21-bioc/R/bin/R CMD INSTALL GeDi ### ############################################################################## ############################################################################## * installing to library ‘/home/biocbuild/bbs-3.21-bioc/R/site-library’ * installing *source* package ‘GeDi’ ... ** this is package ‘GeDi’ version ‘1.4.0’ ** using staged installation ** R ** data ** inst ** byte-compile and prepare package for lazy loading ** help *** installing help indices *** copying figures ** building package indices ** installing vignettes ** testing if installed package can be loaded from temporary location ** testing if installed package can be loaded from final location ** testing if installed package keeps a record of temporary installation path * DONE (GeDi)
GeDi.Rcheck/tests/testthat.Rout.fail
R version 4.5.1 (2025-06-13) -- "Great Square Root" Copyright (C) 2025 The R Foundation for Statistical Computing Platform: x86_64-pc-linux-gnu R is free software and comes with ABSOLUTELY NO WARRANTY. You are welcome to redistribute it under certain conditions. Type 'license()' or 'licence()' for distribution details. R is a collaborative project with many contributors. Type 'contributors()' for more information and 'citation()' on how to cite R or R packages in publications. Type 'demo()' for some demos, 'help()' for on-line help, or 'help.start()' for an HTML browser interface to help. Type 'q()' to quit R. > library(testthat) > library(GeDi) > > test_check("GeDi") trying URL 'https://stringdb-downloads.org/download/protein.aliases.v12.0/9606.protein.aliases.v12.0.txt.gz' preparing gene to GO mapping data... preparing gene to GO mapping data... [ FAIL 8 | WARN 13 | SKIP 0 | PASS 176 ] ══ Failed tests ════════════════════════════════════════════════════════════════ ── Failure ('test-distance_dendro.R:11:3'): distanceDendro runs correctly ────── `dendro` has type 'object', not 'list'. ── Failure ('test-distance_dendro.R:15:3'): distanceDendro runs correctly ────── `dendro` has type 'object', not 'list'. ── Error ('test-downloadPPI.R:2:3'): no id ───────────────────────────────────── Error in `open.connection(file, "rt")`: cannot open the connection to 'https://stringdb-downloads.org/download/species.v12.0.txt' Backtrace: ▆ 1. ├─testthat::expect_true(is.na(getId(""))) at test-downloadPPI.R:2:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─GeDi::getId("") 5. └─utils::read.delim(url(url_species)) 6. └─utils::read.table(...) 7. ├─base::open(file, "rt") 8. └─base::open.connection(file, "rt") ── Error ('test-downloadPPI.R:6:3'): Homo sapiens ID ─────────────────────────── Error in `open.connection(file, "rt")`: cannot open the connection to 'https://stringdb-downloads.org/download/species.v12.0.txt' Backtrace: ▆ 1. ├─testthat::expect_true(getId("Homo sapiens") == "9606") at test-downloadPPI.R:6:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─GeDi::getId("Homo sapiens") 5. └─utils::read.delim(url(url_species)) 6. └─utils::read.table(...) 7. ├─base::open(file, "rt") 8. └─base::open.connection(file, "rt") ── Error ('test-downloadPPI.R:10:3'): Homo Sapiens Misspelled ────────────────── Error in `open.connection(file, "rt")`: cannot open the connection to 'https://stringdb-downloads.org/download/species.v12.0.txt' Backtrace: ▆ 1. ├─testthat::expect_true(is.na(getId("Homo Spasiens"))) at test-downloadPPI.R:10:3 2. │ └─testthat::quasi_label(enquo(object), label, arg = "object") 3. │ └─rlang::eval_bare(expr, quo_get_env(quo)) 4. └─GeDi::getId("Homo Spasiens") 5. └─utils::read.delim(url(url_species)) 6. └─utils::read.table(...) 7. ├─base::open(file, "rt") 8. └─base::open.connection(file, "rt") ── Error ('test-downloadPPI.R:24:3'): PPI retrieval works ────────────────────── Error in `download.file(urlStr, temp)`: cannot open URL 'https://stringdb-downloads.org/download/protein.aliases.v12.0/9606.protein.aliases.v12.0.txt.gz' Backtrace: ▆ 1. └─GeDi::getAnnotation(stringdb) at test-downloadPPI.R:24:3 2. └─stringdb$get_aliases() 3. └─STRINGdb::downloadAbsentFile(...) 4. └─utils::download.file(urlStr, temp) ── Failure ('test-gs_histogram.R:27:3'): gsHistogram runs correctly ──────────── `histogram` has type 'object', not 'list'. ── Failure ('test-gs_histogram.R:30:3'): gsHistogram runs correctly ──────────── `histogram` has type 'object', not 'list'. [ FAIL 8 | WARN 13 | SKIP 0 | PASS 176 ] Error: Test failures Execution halted
GeDi.Rcheck/GeDi-Ex.timings
name | user | system | elapsed | |
GeDi | 0.006 | 0.002 | 0.007 | |
buildClusterGraph | 0.191 | 0.025 | 0.215 | |
buildGraph | 0.006 | 0.001 | 0.008 | |
buildHistogramData | 0.008 | 0.002 | 0.010 | |
calculateJaccard | 0.008 | 0.000 | 0.009 | |
calculateKappa | 0.015 | 0.001 | 0.015 | |
calculateSorensenDice | 0.008 | 0.001 | 0.008 | |
checkInclusion | 0.007 | 0.003 | 0.010 | |
clustering | 0.174 | 0.020 | 0.192 | |
deprecated | 0 | 0 | 0 | |
distanceDendro | 0.208 | 0.012 | 0.219 | |
distanceHeatmap | 0.126 | 0.001 | 0.127 | |
enrichmentWordcloud | 0.229 | 0.006 | 0.236 | |
fuzzyClustering | 0.006 | 0.001 | 0.008 | |
getAdjacencyMatrix | 0.066 | 0.002 | 0.068 | |